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Background: Latinos are currently the largest and fastest growing racial/ethnic group in the United States and have the lowest rates nationally of regular sources of primary care. The changing demographics of Latino populations have significant implications for the future health of the nation, particularly with respect to chronic disease. Community-based agencies and clinics alike have a long history of engaging community health workers (CHWs) to provide a broad range of tangible and emotional support strategies for Latinos with chronic diseases. In this paper, we present the protocol for a community intervention designed to evaluate the impact of CHWs in a Community-Clinical Linkage model to address chronic disease through innovative utilization of electronic health records (EHRs) and application of mixed methodologies. Linking Individual Needs to Community and Clinical Services (LINKS) is a 3-year, prospective matched observational study designed to examine the feasibility and impact of CHW-led Community-Clinical Linkages in reducing chronic disease risk and promoting emotional well-being among Latinos living in three U.S.-Mexico border communities.Methods: The primary aim of LINKS is to create Community-Clinical Linkages between three community health centers and their respective county health departments in southern Arizona. Our primary analysis is to examine the impact of the intervention 6 to 12-months post program entry. We will assess chronic disease risk factors documented in the EHRs of participants versus matched non-participants. By using a prospective matched observational study design with EHRs, we have access to numerous potential comparators to evaluate the intervention effects. Secondary analyses include modeling within-group changes of extended research-collected measures. This approach enhances the overall evaluation with rich data on physical and emotional well-being and health behaviors of study participants that EHR systems do not collect in routine clinical practice.Discussion: The LINKS intervention has practical implications for the development of Community-Clinical Linkage models. The collaborative and participatory approach in LINKS illustrates an innovative evaluation framework utilizing EHRs and mixed methods research-generated data collection.Trial Registration: This study protocol was retrospectively registered, approved, and made available on Clinicaltrials.gov by NCT03787485 as of December 20, 2018. [ABSTRACT FROM AUTHOR]